NAME

Bio::Tradis::Map - Perform mapping

VERSION

version 1.4.5

SYNOPSIS

Takes a reference genome and indexes it. Maps given fastq files to ref.

   use Bio::Tradis::Map;
   
   my $pipeline = Bio::Tradis::Map->new(fastqfile => 'abc', reference => 'abc');
   $pipeline->index_ref();
   $pipeline->do_mapping();

PARAMETERS

Required

"fastqfile" - path to/name of file containing reads to map to the reference
"reference" - path to/name of reference genome in fasta format (.fa)

Optional

"refname" - name to assign to the reference index files. Default = ref.index
"outfile" - name to assign to the mapped SAM file. Default = mapped.sam

METHODS

"index_ref" - create index files of the reference genome. These are required for the mapping step. Only skip this step if index files already exist. -k and -s options for referencing are calculated based on the length of the reads being mapped as per table:
"do_mapping" - map "fastqfile" to "reference". Options used for mapping are: "-r -1 -x -y 0.96"

For more information on the mapping and indexing options discussed here, see the SMALT manual <ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-manual-0.7.4.pdf>

AUTHOR

Carla Cummins <path-help@sanger.ac.uk>

COPYRIGHT AND LICENSE

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007